In a research article titled “DNMT3A and TET2 restrain mitochondrial DNA-mediated interferon signaling in macrophages” published in the journal Immunity on August 4, 2022, an international team led by scientists at the University of California, San Diego, has uncovered a surprising mechanistic link among hardened arteries, inflammation, the integrity of mitochondrial DNA, and mutations in two genes: DNMT3A and TET2.

Age is the predominant risk factor for cardiovascular disease (CVD). This is in part due to the snowballing of environmental risk factors over time, and in part due to risk factors acquired later in life, such as mutations that crop up in blood cells through a process called clonal hematopoiesis—where mutations in immature blood cells give rise to populations of mature blood cells carrying identical mutations.

Mutations in stem cells that specialize into diverse blood cells can confer a competitive growth advantage and result in CHIP (clonal hematopoiesis of indeterminate potential) when not linked to increases in blood cell counts, and blood cancers. Nearly 20% people over 65 years carry mutations in white blood cells that trigger abnormal growth. These mutations nearly double the risk of CVD, with the degree of risk paralleling the frequency of the mutant allele.

Mutations in two cancer-related genes, DNMT3A and TET2, are strong drivers of CHIP. DNMT3A methylates DNA to suppress transcription while TET2 reverses the process, but the biological role of these genes in blood cells remains poorly understood.

In the current study that combines transcriptomic, epigenetic, and imaging assays, scientists investigated the biological roles of DNMT3A and TET2 in normal human macrophages derived from monocytes (mDM) and in mDMs isolated from human atherosclerotic plaques where patients carried mutations in DNMT3A or TET2. They found, in addition to the distinct functions of these genes in regulating gene expression in macrophages, these genes also share a common role in maintaining the integrity of mitochondrial DNA.

Gerald Shadel, PhD, a professor at Salk Institute, and director of the San Diego Nathan Shock Center of Excellence in the Basic Biology of Aging is a co-senior author of the study.

“We found that the genes DNMT3A and TET2, in addition to their normal job of altering chemical tags to regulate DNA, directly activate expression of a gene involved in mitochondrial inflammatory pathways, which hints at a new molecular target for atherosclerosis therapeutics,” said Gerald Shadel, PhD, a professor at Salk Institute, director of the San Diego Nathan Shock Center of Excellence in the Basic Biology of Aging and co-senior author of the study.

Through research that started with the aim of understanding the roles of mutations in DNMT3A and TET2 in clonal hematopoiesis, the authors found DNMT3A and TET2 deficiency in macrophages is related to abnormal inflammatory signaling and consequent atherosclerosis—hardening and narrowing of arteries due to plaque formation.

Christopher Glass, PhD, a professor at the UC San Diego School of Medicine is a co-senior author of the study.

“The problem was we couldn’t work out how DNMT3A and TET2 were involved because the proteins they code do seemingly opposite things regarding DNA regulation,” says Christopher Glass, PhD, a professor at the UC San Diego School of Medicine and co-senior author of the study. “Their antagonistic activity led us to believe there may be other mechanisms at play. This prompted us to take a different approach and contact Shadel, who had uncovered the same inflammatory pathway years earlier while examining responses to mitochondrial DNA stress.”

Shadel’s team had previously found, reduced production of a protein called TFAM (Transcription Factor A, Mitochondria) in mitochondria, causes the expulsion of mitochondrial DNA from the organelle into the cytoplasm, which triggers a cascading alarm system that leads to inflammation.

Glass and Shadel’s teams worked together to better understand why DNMT3A and TET2 mutations led to inflammation as observed during mitochondrial DNA stress. They found, experimentally reducing the expression of DNMT3A or TET2 in normal blood cells increased inflammation, as observed in blood cells from atherosclerosis patients. They then found low levels of DNMT3A and TET2 in blood cells leads to reduced TFAM expression, which in turn leads to abnormal mitochondrial DNA packaging, release of mitochondrial DNA into the cytosol, and inflammation.

Scientists have identified a pathway that could be therapeutically targeted to reduce the risk of cardiovascular disease in patients with mutations in the genes DNMT3A or TET2 [Cobo I, et al, Immunity, 2022.]

“We discovered that DNMT3A and TET2 mutations prevent their ability to bind and activate the TFAM gene,” said Isidoro Cobo, PhD, a postdoctoral researcher in the Glass lab and lead author of the study. “Missing or reducing this binding activity leads to mitochondrial DNA release and an overactive mitochondrial inflammation response, and we believe this may exacerbate plaque buildup in atherosclerosis.”

The study underscores the molecular link between mitochondrial stress induced inflammation and atherosclerosis. The finding could lead to new therapeutic targets in pathways that exacerbate atherosclerosis in patients with TET2A and DNMT3A mutations, to tackle inflammation which is a common cause or symptom for several diseases, including cardiovascular disease. In upcoming studies, the Glass and Shadel’s teams with try to understand how this new mechanism is involved in inflammatory diseases and aging.